During the nineteenth century the Christians in kerala were divided into two groups known as puthenkoor and pazhyakoor. Our founder His Grace Pulikottil Mar Dionasios II wanted a unity between the two groups. For this purpose his grace and Rev. Fr. Mani Nidhierickal formed a society known as “Nasrani Jhathaikai”. This society later paved the foundation of the school. These facts are recorded in the book “malankara nasranikal” written by Sri. Z M Paret. His grace was neoteric in his view and he wanted the church to change to the changing world. His grace wanted to start a school at woodlands estate, he had availed from an Englishman named Darah, who in turn laid the foundation stone for the school in 1888 and had promised to his grace to give help. But his untimely death was a great shock for his grace. So his grace had to endeavor many difficulties to raise his dream into a reality. So his grace made a committee consisting of Sri. Kandathil Varghese Mappilai (secretary), Sri. Pukadiyil Ouseph Itoop, Sri. Kochuvalanzhattil Korah Kurien, Sri. Edavazhikal M Philipose (secretary) for the smooth governing of the school. In 1893 January 30th then kottayam divan Peshkaar Ramah Rayar inaugurated the school.
There were 100 students at the beginning. Many students from distant places were studying at MDSHSS and during that time transportation were rare. so a boarding home was started during the time of Sri V J Itticheria. the school also had prayer hall. now Mar Elia Cathedral is situated in this same site. In 1958 the MDS high school was elevated as Higher Secondary, but due to new education policy of the then Kerala Government, the status co was removed.
The organisied facilities that were built for the working of higher secondary was then given to then founded Baselius College in1964, including the land and buildings. The year 1964 is very important in the history of MDSHSS. It was in this year the school was moved to the current location. During this period the first lady teacher Smt. V M Savathriamma joined here. Then headmaster Sri K C John also took a bold decision to admit girls to this school It was in 1959 the school started the magazine “Dionysian” so that the students could express their thoughts to the outside world. in 1973 then principal Rev. Fr. M M Jacob later ordained as His Grace Yacoob Mar Polycarpos renamed boarding home as Mar Augen Boarding Home in memorial of late His Holiness Baselius Mar Augen I Catholicos. The upper primary building's foundation stone was laid by His Holiness Moran Mar Baselius Marthoma Mathews I on 29th September 1988 and the centenary building's foundation stone was laid on 30th January 1992 by His Holiness Moran Mar Baselius Marthoma Mathews II.
The centenary building complex was completed in 1994 during the time of Headmaster Sri. K K Abraham Puthenkavu and inaugurated on 28th February 1994 by His Holiness Moran Mar Baselius Marthoma Mathews II. and consecrated by His Grace Thomas Mar Athanasios then School Manager. In 1998 MDSHS was again promoted as MD Seminary Higher Secondary School with two science batches and one commerce batch. In the year 2000 more batches were allotted to the school .The foundation stone for the new building complex for the higher secondary section was laid in 2001 during the time of Smt. Marius Sleeba and the work started and completed during the tenure of Sri. C K Mathai